International Institutional Awards Tranche 1 Quadram
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Department Name: Food Innovation and Health
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Organisations
- QUADRAM INSTITUTE BIOSCIENCE (Lead Research Organisation)
- University of Turin (Collaboration)
- North Carolina State University (Collaboration)
- Carl von Ossietzky University of Oldenburg (Collaboration)
- Swiss Institute of Bioinformatics (SIB) (Collaboration)
- University College London (Collaboration)
- University of Verona (Collaboration)
People |
ORCID iD |
| Martin Warren (Principal Investigator) |
Publications
Kolenc Ž
(2024)
Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea.
in The Science of the total environment
| Description | 1. Establishing and Strengthening Collaborations Initiated discussions with Wageningen, INRAE, University of Copenhagen, and University of Valencia for joint projects. Formalized collaborations through Memorandums of Understanding (MOUs) with NABI and Liggins Institute (focused on fecal microbiome transplantation, FMT). Engaged in ongoing discussions for joint funding applications (UKRI, European) and PhD studentships. Fostered bilateral relationships between principal investigators (PIs) across institutions. 2. Advancing Research and Innovation Developed protocols for genetic transformation and mutagenesis of F. nucleatum. Established new methodologies in molecular microbiology, glycan analysis, and bacterial sequencing. Expanded bioinformatics capabilities from sequence-based to protein-based and AI-enhanced applications. Implemented metabuli into Galaxy (a key bioinformatics tool). Developed One Food Risk Tool prototype to assess food system risks during net-zero transitions. 3. Knowledge Exchange and Capacity Building Organized multiple high-impact workshops, including: "Horizon Europe: Funding & Grant Management" "Next-level Grant Writing Using AI Assistants" "Large Scale Analysis of Microbial Genomes" Nutrition in Neonates Delivered training in advanced metagenomics, including: Processing and sequencing of 180 microbiome samples (mother, infant, and child). Advanced metagenome analysis and epidemiological metadata assessment. Upskilled early-career researchers and postdocs through international exchanges and bioinformatics training. Strengthened clinical trial management expertise through visits to NIH and USDA. 4. Enhancing QIB's Research and Infrastructure Insights gained from USDA dietary intervention suite for improving QIB facilities. NIH visit provided methods to enhance QIB clinical trials. Strengthened expertise in glycoimmunology, CRISPR, and organoid technologies. Advanced knowledge and licensing strategies for FMT facilities. 5. Publications and Future Research One paper already published (DOI: 10.3390/foods13132005), with others in preparation. Collaborative paper in progress on bacteriophage diversity in farm environments. Roundtable discussion led to a paper on nutrition vulnerability and net-zero transition (in preparation for Nutrition Bulletin). Initiated a project expanding viral gene catalogues using AI-derived protein structures. 6. Industry and Policy Impact Engaged with food industry partners for research on safety of fermented soy products. Convened a roundtable on food security and nutrition risks in net-zero transitions. Strengthened strategic relationships with USDA and industry leaders. |
| Exploitation Route | This grant has significantly broadened QIB's international reach, enhanced research capacity, fostered new collaborations, and contributed to high-impact scientific advancements. This has resulted in new on-going collaborations that will result in further research and innovation. |
| Sectors | Agriculture Food and Drink Education Healthcare |
| Description | Some of the interactions that have been forged as a result of this grant have been used to help develop clinical practice especially with respect to food trials. Other interactions have led to contributions in developing policy tools on hazards related to the food system which can be used by governments across the world. Similarly, stronger links with the US CDC have been developed by capitalising on a partnership with Cefas, which works on food safety and has global links. |
| Sector | Agriculture, Food and Drink,Education,Healthcare |
| Impact Types | Societal Policy & public services |
| Description | AI and Protein structure |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Hosted a discussion on AI an microbial genomics, identifying LLMs applied to protein sequences as an under explored target. |
| Collaborator Contribution | Delivered a seminar and contributed to capacity building |
| Impact | In collaboration with Dr Evelien Adriaenssens (QIB), we are developing a pipeline to core genome identification using the AI methods emerged during this collaboration |
| Start Year | 2024 |
| Description | Anvi'o: exploring pangenome and metagenomes |
| Organisation | Carl von Ossietzky University of Oldenburg |
| Department | Helmholtz Institute for Functional Marine Biodiversity |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Organised workshops and round-tables, delivered training |
| Collaborator Contribution | Delivered seminars and hands-on workshops on Anvi'o |
| Impact | Training materials; Contributed to a poster presented in South Africa (August 2024) at the ISME; Prepared materials for a workshop in Brest (October 2024) |
| Start Year | 2024 |
| Description | Machine Learning applied to microbial datasets |
| Organisation | University of Turin |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | Our research team worked with Dr. Giovanni Birolo during his visit to the Quadram Institute, focusing on the application of machine learning techniques to microbial genomics. Together, we embarked on a project that integrated Dr. Birolo's background in mathematics and computer science with our team's ongoing research in microbial genomics and metabarcoding datasets. Our contributions: 1) Data Preparation and Provision: We provided comprehensive metabarcoding datasets, which included a wide variety of microbial genomic sequences. Our team was responsible for collecting, curating, and pre-processing these datasets with in-house developed pipelines to ensure they were suitable for machine learning analysis, which was crucial for the success of the workshop and subsequent research activities. 2) Expertise in Microbial Genomics: We offered insights into the biological significance and potential applications of the machine learning models developed during the collaboration. This allowed for a more targeted approach in the analysis and interpretation of the data, leading to more biologically meaningful outcomes. 3) Technical Support and Infrastructure: We facilitated access to the necessary computational resources and infrastructure required for the intensive computational tasks associated with machine learning and data analysis. This included high-performance computing facilities and software tools tailored for bioinformatics research and our own QIB Cloud infrastructure. 4) Workshop Organization and Participation: Our team organized a workshop titled "Random Forests and Cross-Validation on a Metabarcoding Dataset," delivered by Dr. Birolo. We contributed to the workshop's content by providing case studies and examples from our research. Furthermore, our team actively participated in the workshop, engaging in discussions, sharing insights, and fostering a collaborative learning environment for all participants. See https://github.com/quadram-institute-bioscience/datasciencegroup/blob/main/4_machine_learning/Prediction-notes.ipynb |
| Collaborator Contribution | 1) Expertise in Machine Learning: Dr. Birolo introduced advanced machine learning techniques, particularly random forests and cross-validation methods, tailored for the analysis of complex metabarcoding datasets. His deep understanding of these computational approaches enabled our team to adopt more sophisticated analytical strategies, significantly enhancing our ability to decipher microbial genomic data. 2) Workshop Delivery: Dr. Birolo delivered an insightful workshop titled "Random Forests and Cross-Validation on a Metabarcoding Dataset," which was instrumental in upskilling our research team. This workshop provided theoretical knowledge and included practical sessions on applying these machine-learning techniques to real-world datasets, fostering a hands-on learning environment. 3) Novel Analytical Frameworks: By integrating his mathematical and bioinformatics expertise, Dr. Birolo contributed to the development of novel analytical frameworks that improved the accuracy and efficiency of identifying and classifying microbial species from metabarcoding data. This advancement has the potential to greatly impact the field of microbial genomics, opening up new avenues for research and application. |
| Impact | 1) Workshop material (see link) 2) Engagement with researchers to define the application of Machine Learning on microbial genomics datasets 3) Primed a collaboration on software development (ongoing) |
| Start Year | 2024 |
| Description | Metaproteomics-SIP to determine nitrogen sharing in the human gut |
| Organisation | North Carolina State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Prof Manuel Kleiner at NC State University (US) |
| Collaborator Contribution | Prof Kleiner and I have established a network between US and UK to exchange knowledge of how protein impacts human health. Specifically, they will analyse my in vitro incubation using metaproteomics combined with stable isotope probing. |
| Impact | Preliminary proteomic datasets |
| Start Year | 2024 |
| Description | Peta-scale analysis of microbial genomes |
| Organisation | Swiss Institute of Bioinformatics (SIB) |
| Country | Switzerland |
| Sector | Charity/Non Profit |
| PI Contribution | Organised a workshop (3 days), brought microbial genomics expertise on a discussion with a research-group mostly focussed on eukaryotic genomes. |
| Collaborator Contribution | Delivered seminars and workshops on OMA |
| Impact | There are ongoing research projects started from this workshop, one including partners as co-authors. |
| Start Year | 2024 |
| Description | Statistical methods for Microbiome analysis |
| Organisation | University of Verona |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | Delivered well-attended workshops on microbiome analysis at the Quadram institute, covering rarefaction and benchmarking of methods for differential abundance of features. |
| Collaborator Contribution | Delivered 2 workshops at QIB |
| Impact | Online chapter: https://mcalgaro93.github.io/randomtopics/rarefaction-practice-in-microbiome-data-analysis.html |
| Start Year | 2024 |
| Title | FASTX::Reader perl module for FASTX parsing |
| Description | Pure-perl module to parse FASTA and FASTQ files, gzipped. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Updated during the IAA collaboration to improve support for phage annotation, re-instating Genetic Code 15 that was removed from NCBI Genetic Code tables. This was implemented in Metaprokka, and improved DNA translation for phage annotation. |
| URL | https://metacpan.org/dist/FASTX-Reader |
| Title | Metaprokka |
| Description | A fork of "prokka" focused on improving annotation results when analysing phage genomes (or metagenomes including virome) |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | A publication (https://pmc.ncbi.nlm.nih.gov/articles/PMC11210395/) where the impact of using appropriate genetic codes for gene prediction in phages was analysed. Metaprokka implements the methods and allows others to apply it to their datasets. |
| URL | https://bioconda.github.io/recipes/metaprokka/README.html |
| Title | seqfu-amplify |
| Description | In silico amplification using degenerate primers |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Used for systematic extraction of 16S amplicons from genomes and MAGs |
| URL | https://github.com/telatin/seqfu-amplify |
| Description | Anvi'o Workshop 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | 40 researchers at different career stage engaged with the authors of Anvi'o to learn how to curate and explore pangenomes, metagenomes and metabolic pathways datasets. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://corebio.info/workshops-2024/anvio |
| Description | Building Bridges Website |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website to promote the workshops organised by Lisa Marchioretto thanks to this award. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://lmarchio.github.io/building-bridges/ |
| Description | EUBiome visit at QIB |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | QIB hosted a visit from EUbiome's CEO and bioinformatician, which included a seminar on building successful startups. This visit facilitated discussions around fecal microbiome transplant research and identified potential areas for collaboration. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Horizon Europe: Funding Opportunities, Application Strategies, and Grant Management |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | QIB organized a two-day workshop, "Horizon Europe: Funding Opportunities, Application Strategies, and Grant Management," featuring expert speakers from various European institutions. This event provided comprehensive guidance on navigating EU funding programs, with a focus on building networks, identifying suitable calls, and managing grants effectively. he Horizon Europe workshop equipped staff with skills for navigating EU funding landscapes, enhancing QIB's competitiveness in securing grants. QIB gained insights into EU funding mechanisms and grant management practices from experienced European institutions like the University of Bologna, University of Padua, University of East Anglia and University College Cork. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://lmarchio.github.io/building-bridges/horizon |
| Description | Invited talk at NC State - "Friend or foe - The sulphide-producing bacteria within you" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited lecture at North Carolina State University by my collaborator Associate Professor Manuel Kleiner. This was the kickoff meeting for my BBSRC Discovery Fellowship. The location was Microbiomes and Complex Microbial Communities Cluster. Thomas Hall 4510B |
| Year(s) Of Engagement Activity | 2024 |
| Description | Knowledge exchange visit to Agriculture and AgriFood Canada |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Visit of UK researchers to the Canadian government organisation Agriculture and AgriFood Canada (AAFC). UK PIs gave a presentation about the work happening at the Quadram Institute to research scientists, stimulating debate into potential alignment of future research. |
| Year(s) Of Engagement Activity | 2024 |
| Description | MAK participation in FoodForce Event, Brussels |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A QIB representative visited Brussels to engage with potential collaborators, successfully initiating conversations with Wageningen, INRAE, UniCopenaghen and UniValencia about possible joint projects. These activity has broadened QIB's international network, creating a robust foundation for future collaborations and knowledge exchange in key research areas. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Next-level grant writing using AI assistants |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The workshop "Next-level grant writing using AI assistants" was held to explore innovative approaches to proposal development using artificial intelligence tools. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://lmarchio.github.io/building-bridges/ai |
| Description | nf-core hackathon 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Local site of "nf-core" hackathon to improve the open source pipelines and documentation from the nf-core organization |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://corebio.info/workshops-2024/nf-core |